Flow chart of the analytic approach to identify lineage-specific biomarker levels.

<p><b>A:</b> differences in biomarker levels were sorted as specific to (i) humans, (ii) great apes, (iii) bonobos, (iv) chimpanzees, (v) Central African chimpanzees, (vi) West African chimpanzees and as (vii) non-lineage specific. <b>B:</b> Human-specific changes were defined as significant differences to chimpanzees and bonobos taken together (but not between the latter two species) as well as to rhesus macaques (shown); and as significant differences between humans and the individual great ape species (not shown), regardless of significant differences between species born and living under different environments. Relations of species as shown in cladograms derived from [<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0134548#pone.0134548.ref103" target="_blank">103</a>, <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0134548#pone.0134548.ref104" target="_blank">104</a>].</p

Lineage-Specific Changes in Biomarkers in Great Apes and Humans

<div><p>Although human biomedical and physiological information is readily available, such information for great apes is limited. We analyzed clinical chemical biomarkers in serum samples from 277 wild- and captive-born great apes and from 312 healthy human volunteers as well as from 20 rhesus macaques. For each individual, we determined a maximum of 33 markers of heart, liver, kidney, thyroid and pancreas function, hemoglobin and lipid metabolism and one marker of inflammation. We identified biomarkers that show differences between humans and the great apes in their average level or activity. Using the rhesus macaques as an outgroup, we identified human-specific differences in the levels of bilirubin, cholinesterase and lactate dehydrogenase, and bonobo-specific differences in the level of apolipoprotein A-I. For the remaining twenty-nine biomarkers there was no evidence for lineage-specific differences. In fact, we find that many biomarkers show differences between individuals of the same species in different environments. Of the four lineage-specific biomarkers, only bilirubin showed no differences between wild- and captive-born great apes. We show that the major factor explaining the human-specific difference in bilirubin levels may be genetic. There are human-specific changes in the sequence of the promoter and the protein-coding sequence of uridine diphosphoglucuronosyltransferase 1 (UGT1A1), the enzyme that transforms bilirubin and toxic plant compounds into water-soluble, excretable metabolites. Experimental evidence that UGT1A1 is down-regulated in the human liver suggests that changes in the promoter may be responsible for the human-specific increase in bilirubin. We speculate that since cooking reduces toxic plant compounds, consumption of cooked foods, which is specific to humans, may have resulted in relaxed constraint on UGT1A1 which has in turn led to higher serum levels of bilirubin in humans.</p></div

Liver UDP-glucuronosyltransferase 1A1 (UGT1A1) promoter transcript expression in rhesus macaques, chimpanzees and humans [47] and respective TATAA-box length [56, 57, 105]

<p>- UGT1A1 transcript expression was determined from RNA-Seq of human, chimpanzee and rhesus macaque liver RNA samples from 3 males and 3 females of each species [<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0134548#pone.0134548.ref047" target="_blank">47</a>]. Relative expression levels were calculated from the original dataset setting human expression levels at 100 percent (also see <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0134548#pone.0134548.s007" target="_blank">S1 Table</a> for the variability of TA repeats in TATA box of UGT1A1 promoter in archaic hominins, humans and non-human primates).</p

Lineage-specific biomarker levels in humans and other primates

<p>- box representing 25th, 50th and 75th percentiles; whiskers representing 2.5^th to 97.5^th percentiles; outliers are not shown; description of species: Rh—DE: captive-born rhesus macaque samples from Germany; B—CD: wild-born bonobo samples from the Democratic Republic of the Congo; B—DE: captive-born bonobo samples from Germany; Ch—CG: wild-born Central African chimpanzee samples from the Republic of Congo; Ch—SL: wild-born West African chimpanzee samples from Sierra Leone; Ch—DE: captive-born West African chimpanzee samples Germany; H—DE: human samples from Germany; A: Bonobo-specific change in apolipoprotein A-I; human-specific change in B: bilirubin, C: cholinesterase and D: lactate; for determination of bilirubin, 1.71 μmol/L represents the lower limit of quantification of the assay.</p

Liver <i>UGT1A1</i>-mRNA expression in mice on raw and cooked diets:

<p>Liver mRNA expression of UGT1A1 transcripts in mice fed either a raw or cooked meat or raw or cooked or tuber diets was measured by RNA-Seq [<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0134548#pone.0134548.ref049" target="_blank">49</a>]. Total RNA was prepared from 17 individuals and sequenced as a pool on two lanes of an Illumina HiSeq 2500. Significant differences in expression between mice fed raw diets and mice fed cooked diets were quantified using DESeq [<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0134548#pone.0134548.ref048" target="_blank">48</a>].</p